(Not a full answer, but maybe helpful)
For the mid
+ Thunderbird part of your question (however, please note that I didn’t test these add-ons yet, so I’m not sure if they really use mid
URIs or some proprietary protocol):
The description of the Thunderbird add-on ThunderLink says (bold by me):
ThunderLink lets you link to email messages in Thunderbird.
[…]
ThunderLinks are based on the unique message ID generated when an email is sent.
The companion Firefox add-on ThunderLinkSpotter
[…] enables the browser to recognize ThunderLinks and turn them into hyperlinks.
Another Thunderbird add-on is MessageID-Finder, which allows to open mails by right-clicking on a message-id (see a screenshot on the website). But this would only work from within Thunderbird.